# \#tree **URL:** https://forum.qiime2.org/tag/tree/131.md [Latest](https://forum.qiime2.org/latest.md) · [Categories](https://forum.qiime2.org/categories.md) · [Tags](https://forum.qiime2.org/tags.md) --- ## [Phylogenetic tree: Reconstruct vs. Prune - When to?](https://forum.qiime2.org/t/phylogenetic-tree-reconstruct-vs-prune-when-to/33753)
**Author:** [@AviTil](https://forum.qiime2.org/u/AviTil)\ **Replies:** 6\ **Last updated:** [November 15, 2025, 6:57am UTC](https://forum.qiime2.org/t/phylogenetic-tree-reconstruct-vs-prune-when-to/33753 "2025-11-15T06:57:54Z")
Hi, This is a relatively simple question. When does one choose to reconstruct a tree vs. prune a phylogenetic tree? Are constructed trees comparable? Say I perform a meta-analysis, and I have a large collection of stu… --- ## [Placing filtered ASV sequences into guide tree, per clade](https://forum.qiime2.org/t/placing-filtered-asv-sequences-into-guide-tree-per-clade/32260)
**Author:** [@morien](https://forum.qiime2.org/u/morien)\ **Replies:** 3\ **Last updated:** [January 10, 2025, 11:38am UTC](https://forum.qiime2.org/t/placing-filtered-asv-sequences-into-guide-tree-per-clade/32260 "2025-01-10T11:38:05Z")
Many years ago, I used to use QIIME 1 with pynast to filter sequence sets prior to EPA placement with RAxML (now I would use epa-ng), and I'm looking for a practical way to do this now. inputs: a set of ASVs that are pr… --- ## [Error occured while running for MAFFT in qiime2](https://forum.qiime2.org/t/error-occured-while-running-for-mafft-in-qiime2/29269)
**Author:** [@pulak](https://forum.qiime2.org/u/pulak)\ **Replies:** 7\ **Last updated:** [February 22, 2024, 4:35pm UTC](https://forum.qiime2.org/t/error-occured-while-running-for-mafft-in-qiime2/29269 "2024-02-22T16:35:31Z")
The following problem occured while running for MAFFT sequence alignment for rep-seqs.qza file in HPC. "Plugin error from phylogeny: Command '\['mafft', '--preservecase', '--inputorder', '--thread', '1', '/tmp/qiime2/pu… --- ## [ASVs of the same genus in different branches on the phylogenetic tree](https://forum.qiime2.org/t/asvs-of-the-same-genus-in-different-branches-on-the-phylogenetic-tree/29293)
**Author:** [@eraysahin](https://forum.qiime2.org/u/eraysahin)\ **Replies:** 2\ **Last updated:** [February 19, 2024, 5:54pm UTC](https://forum.qiime2.org/t/asvs-of-the-same-genus-in-different-branches-on-the-phylogenetic-tree/29293 "2024-02-19T17:54:24Z")
Hello, I constructed my phylogenetic tree using "qiime phylogeny align-to-tree-mafft-fasttree", and exported rooted tree. For taxonomic assignment of the ASVs, I produced weighted classifier of SILVA 138 SSURef NR99. Af… --- ## [What type of database to use for q2-fragment-insertion](https://forum.qiime2.org/t/what-type-of-database-to-use-for-q2-fragment-insertion/27319)
**Author:** [@aghudson](https://forum.qiime2.org/u/aghudson)\ **Replies:** 12\ **Last updated:** [September 8, 2023, 3:37pm UTC](https://forum.qiime2.org/t/what-type-of-database-to-use-for-q2-fragment-insertion/27319 "2023-09-08T15:37:26Z")
Hi, I would like to use the q2-fragment-insertion plugin to create a more robust phylogenetic tree for alpha and beta diversity analysis of my 16S V4 data. Having read through the information at https://library.qiime2.… --- ## [Export phyloseq tree to qiime2](https://forum.qiime2.org/t/export-phyloseq-tree-to-qiime2/26969)
**Author:** [@Nelly](https://forum.qiime2.org/u/Nelly)\ **Replies:** 2\ **Last updated:** [July 8, 2023, 6:56pm UTC](https://forum.qiime2.org/t/export-phyloseq-tree-to-qiime2/26969 "2023-07-08T18:56:12Z")
Hi, I have a Phyloseq object and I am interested in exporting the Phyloseq tree to QIIME2. Since I created the Phyloseq object from WGS data, I wasn't able to take the sequences and construct a phylogenetic tree based o… --- ## [issues moving between greengenes classification and diversity metrics](https://forum.qiime2.org/t/issues-moving-between-greengenes-classification-and-diversity-metrics/25972)
**Author:** [@AttilaTheBun](https://forum.qiime2.org/u/AttilaTheBun)\ **Replies:** 3\ **Last updated:** [March 30, 2023, 1:01pm UTC](https://forum.qiime2.org/t/issues-moving-between-greengenes-classification-and-diversity-metrics/25972 "2023-03-30T13:01:39Z")
Hello all! I'm having some issues with my code, and I'm using greengenes 13\_8 for my reference data, which I realize is highly supported in QIIME2 so I'm sure this is a user-end ignorance issue, but any help is appreciat… --- ## [Beta Diversity Profiling & Significance Testing](https://forum.qiime2.org/t/beta-diversity-profiling-significance-testing/24597)
**Author:** [@cgpeh](https://forum.qiime2.org/u/cgpeh)\ **Replies:** 11\ **Last updated:** [November 1, 2022, 1:41pm UTC](https://forum.qiime2.org/t/beta-diversity-profiling-significance-testing/24597 "2022-11-01T13:41:41Z")
Hi everyone, Newbie here. I am looking a way for significant test of my pcoa plot. So I have generated the core-metrics-results for unweighted and weighted unifrac pcoa plot. I can view the emperor.qzv plot in qiime2.… --- ## [Remove reference tree from fragment insertion tree](https://forum.qiime2.org/t/remove-reference-tree-from-fragment-insertion-tree/23441)
**Author:** [@a\_staubus](https://forum.qiime2.org/u/a_staubus)\ **Replies:** 5\ **Last updated:** [June 27, 2022, 1:38pm UTC](https://forum.qiime2.org/t/remove-reference-tree-from-fragment-insertion-tree/23441 "2022-06-27T13:38:36Z")
Hello! I just used fragment-insertion to generate a tree following this tutorial. I used Silva 128 as a reference tree. After viewing the output in a phylogenetic tree viewer, I realized that the tree that it generates … --- ## [Importing table and tree with spaces in IDs leads to mismatch](https://forum.qiime2.org/t/importing-table-and-tree-with-spaces-in-ids-leads-to-mismatch/20537)
**Author:** [@jwdebelius](https://forum.qiime2.org/u/jwdebelius)\ **Replies:** 2\ **Last updated:** [August 25, 2021, 6:19am UTC](https://forum.qiime2.org/t/importing-table-and-tree-with-spaces-in-ids-leads-to-mismatch/20537 "2021-08-25T06:19:11Z")
I've been using the GTDB tree/kraken 2 table recently. The genome IDs contain underscores in their names. When i import my table into QIIME as a FeatureTable\[Frequency\] (so biom under the hood), the underscores in the na… --- ## [Need some help with phylogenetic diversity and other metrics](https://forum.qiime2.org/t/need-some-help-with-phylogenetic-diversity-and-other-metrics/19257)
**Author:** [@gabrielcoppo](https://forum.qiime2.org/u/gabrielcoppo)\ **Replies:** 1\ **Last updated:** [April 19, 2021, 2:35pm UTC](https://forum.qiime2.org/t/need-some-help-with-phylogenetic-diversity-and-other-metrics/19257 "2021-04-19T14:35:39Z")
Hey, I have some doubts. I used dada2 to denoise my data and followed the "moving pictures" tutorial to generate the outputs. I already generated the .qza for the rooted and unrooted trees and the core-metrics director… --- ## [How to make a phylogenetic tree looking too complex more readable?](https://forum.qiime2.org/t/how-to-make-a-phylogenetic-tree-looking-too-complex-more-readable/12712)
**Author:** [@Sparkle](https://forum.qiime2.org/u/Sparkle)\ **Replies:** 8\ **Last updated:** [December 4, 2019, 3:01pm UTC](https://forum.qiime2.org/t/how-to-make-a-phylogenetic-tree-looking-too-complex-more-readable/12712 "2019-12-04T15:01:43Z")
Hello, I'm trying to create a phylogenetic tree from my representative sequences resulting from a previously performed dada2 analysis, as follows (I'm following this tutorial). qiime alignment mafft --i-sequences rep-… --- ## [iqtree error for unrooted tree in phylogeny](https://forum.qiime2.org/t/iqtree-error-for-unrooted-tree-in-phylogeny/12417)
**Author:** [@sahin\_srhn](https://forum.qiime2.org/u/sahin_srhn)\ **Replies:** 1\ **Last updated:** [November 11, 2019, 2:52pm UTC](https://forum.qiime2.org/t/iqtree-error-for-unrooted-tree-in-phylogeny/12417 "2019-11-11T14:52:47Z")
Hello, I am using Nanopore 16s rRNA data for metagenomics analyses. Since i cant go on from the DADA2 i use the mothur untill the taxonomic classifications. However, i want to use the qiime2 for beta diversity analyses … --- ## [QIIME2R -\> trouble with phyloseq and rooted tree](https://forum.qiime2.org/t/qiime2r-trouble-with-phyloseq-and-rooted-tree/12052)
**Author:** [@ben](https://forum.qiime2.org/u/ben)\ **Replies:** 8\ **Last updated:** [October 28, 2019, 5:29pm UTC](https://forum.qiime2.org/t/qiime2r-trouble-with-phyloseq-and-rooted-tree/12052 "2019-10-28T17:29:50Z")
Hi all, Strange behavior, which wasn't happening when I used the QIIME2R prior, but I am having issues now. I have a merged file w/ 5 different runs. I merged these runs and filtered the file. I then created a tree wit… --- ## [When to make the phylogenetic tree](https://forum.qiime2.org/t/when-to-make-the-phylogenetic-tree/10954)
**Author:** [@rlm](https://forum.qiime2.org/u/rlm)\ **Replies:** 1\ **Last updated:** [August 6, 2019, 9:26pm UTC](https://forum.qiime2.org/t/when-to-make-the-phylogenetic-tree/10954 "2019-08-06T21:26:17Z")
Hi all, I am looking for suggestions regarding when you should make a phylogenetic tree. I used deblur to process my dataset. Should the tree be made with the rep-seqs from the deblur output? After deblur, I removed mit… --- ## [Fix required: Tips in a tree detected as repeated](https://forum.qiime2.org/t/fix-required-tips-in-a-tree-detected-as-repeated/10184)
**Author:** [@rodrigogarlop](https://forum.qiime2.org/u/rodrigogarlop)\ **Replies:** 4\ **Last updated:** [June 25, 2019, 6:11pm UTC](https://forum.qiime2.org/t/fix-required-tips-in-a-tree-detected-as-repeated/10184 "2019-06-25T18:11:23Z")
Hi I have been using QIIME 1 for a while now and I'm finally switching to QIIME2 out (v 2019.1). I was trying to compare Q1 and Q2 OTUs with ASVs but I'm having some problems when running Sepp for the phylogenies constr… --- ## [Alignment/Tree Building and Filtering samples](https://forum.qiime2.org/t/alignment-tree-building-and-filtering-samples/8687)
**Author:** [@ejunkins](https://forum.qiime2.org/u/ejunkins)\ **Replies:** 2\ **Last updated:** [March 13, 2019, 9:27pm UTC](https://forum.qiime2.org/t/alignment-tree-building-and-filtering-samples/8687 "2019-03-13T21:27:02Z")
Hello, I am running Q2-2018.6. I imported featuredata\[sequence\] and featuretable\[frequency\] from USEARCH. That run contains multiple projects and I wish to split it by sample. Should I do this before I build the mafft a… --- ## [Filter representative FASTA sequences](https://forum.qiime2.org/t/filter-representative-fasta-sequences/8340)
**Author:** [@Nasute](https://forum.qiime2.org/u/Nasute)\ **Replies:** 3\ **Last updated:** [February 13, 2019, 6:06pm UTC](https://forum.qiime2.org/t/filter-representative-fasta-sequences/8340 "2019-02-13T18:06:21Z")
Dear members of the community Perform the sequencing of 4 samples with the marker RNA16s. To build the phylogenetic tree I did it following the tutorial "Moving Pictures", however my phylogenetic tree shows many polytom… --- ## [Software to visualize the tooted-tree. qza file](https://forum.qiime2.org/t/software-to-visualize-the-tooted-tree-qza-file/5582)
**Author:** [@idapantoja](https://forum.qiime2.org/u/idapantoja)\ **Replies:** 1\ **Last updated:** [August 15, 2018, 1:18am UTC](https://forum.qiime2.org/t/software-to-visualize-the-tooted-tree-qza-file/5582 "2018-08-15T01:18:53Z")
Hi! Wondering what softwares do you recommend to visualize the rooted-tree.qza. I tried FigTree but it didn't work. Maybe it is because of the format .qza. Is there any option I can try uploading the artifact directly … --- ## [What to do about a single non-corresponding tree tip?](https://forum.qiime2.org/t/what-to-do-about-a-single-non-corresponding-tree-tip/5364)
**Author:** [@EmerickL](https://forum.qiime2.org/u/EmerickL)\ **Replies:** 3\ **Last updated:** [August 3, 2018, 1:20pm UTC](https://forum.qiime2.org/t/what-to-do-about-a-single-non-corresponding-tree-tip/5364 "2018-08-03T13:20:27Z")
Greetings Qiime community, I typically do analysis in R after classification, tree building and BIOM exporting but am giving QIIME2's other features a go. I am starting with alpha and beta diversity metrics but have run… --- ## [Collapsing phylogenetic tree](https://forum.qiime2.org/t/collapsing-phylogenetic-tree/4264)
**Author:** [@epark](https://forum.qiime2.org/u/epark)\ **Replies:** 1\ **Last updated:** [May 23, 2018, 3:31pm UTC](https://forum.qiime2.org/t/collapsing-phylogenetic-tree/4264 "2018-05-23T15:31:03Z")
Hello. I collapsed my feature table using plugin qiime taxa collapse to generate genus level (level 6) feature table. Now I am trying to do beta diversity UniFrac using the genus-level feature table. However, for doing … --- ## [Error phylogen (fasttree)](https://forum.qiime2.org/t/error-phylogen-fasttree/4227)
**Author:** [@Nasute](https://forum.qiime2.org/u/Nasute)\ **Replies:** 1\ **Last updated:** [May 21, 2018, 11:04pm UTC](https://forum.qiime2.org/t/error-phylogen-fasttree/4227 "2018-05-21T23:04:11Z")
Hi Everyone! Hello, I am all experiencing a problem with the creation of a phylogenetic tree using the "fasttree" program since I apparently have an (excess of arguments) however, I am using the parameters that come by … --- ## [After qiime phylogeny filter-table does one need qiime phylogeny "filter-sequence"?](https://forum.qiime2.org/t/after-qiime-phylogeny-filter-table-does-one-need-qiime-phylogeny-filter-sequence/3486)
**Author:** [@Paul\_Czechowski](https://forum.qiime2.org/u/Paul_Czechowski)\ **Replies:** 2\ **Last updated:** [March 21, 2018, 2:36pm UTC](https://forum.qiime2.org/t/after-qiime-phylogeny-filter-table-does-one-need-qiime-phylogeny-filter-sequence/3486 "2018-03-21T14:36:15Z")
Dear Qiime develepment team, My questions is: Does alignment masking remove sequences? If so then running qiime phylogeny filter-table ... would be necessary, as I did it here (below). If so then the unaligned sequen… --- ## [Loading Greengenes tree in iTOL](https://forum.qiime2.org/t/loading-greengenes-tree-in-itol/2319)
**Author:** [@Richard\_Rodrigues](https://forum.qiime2.org/u/Richard_Rodrigues)\ **Replies:** 10\ **Last updated:** [February 13, 2018, 9:48pm UTC](https://forum.qiime2.org/t/loading-greengenes-tree-in-itol/2319 "2018-02-13T21:48:30Z")
Hi, Did anyone figure out the solution for this? Basically, 97\_otus tree can be visualized in ITOL, but it seems the internal ids and annotation already in the tree are not being recognized by ITOL. Adding an external a… --- ## [File conversion](https://forum.qiime2.org/t/file-conversion/2554)
**Author:** [@Jasmine84](https://forum.qiime2.org/u/Jasmine84)\ **Replies:** 2\ **Last updated:** [February 2, 2018, 1:11pm UTC](https://forum.qiime2.org/t/file-conversion/2554 "2018-02-02T13:11:30Z")
Hello I would like to visualize my phylogenetic trees using https://itol.embl.de/ as you do not have a visualization tools for this in QIIME2. But first I have to convert the file to for example a txt file. How do I do… --- ## [From qiime2 to R : how to transform a .qza to .tre](https://forum.qiime2.org/t/from-qiime2-to-r-how-to-transform-a-qza-to-tre/2670)
**Author:** [@leila](https://forum.qiime2.org/u/leila)\ **Replies:** 2\ **Last updated:** [January 22, 2018, 9:24pm UTC](https://forum.qiime2.org/t/from-qiime2-to-r-how-to-transform-a-qza-to-tre/2670 "2018-01-22T21:24:27Z")
Hi, I would like to export my rooted-tree.qza in R and work with phyloseq. For this I would need .tre format for the three. How can you export your .qza in .tre? Thank you very much, Leila --- ## [Phylogenetic table with lablels](https://forum.qiime2.org/t/phylogenetic-table-with-lablels/2668)
**Author:** [@arsalane1978](https://forum.qiime2.org/u/arsalane1978)\ **Replies:** 1\ **Last updated:** [January 22, 2018, 9:20pm UTC](https://forum.qiime2.org/t/phylogenetic-table-with-lablels/2668 "2018-01-22T21:20:18Z")
Dear Qiime2 team / users, Thank you for maintaining and updating the forum. I have a naive question as a new commercial to the field. Is there any way to visualize the fast tree rooted tree while labels are actual sci… --- ## [How to build a tree with tips collapsed based on the taxonomic classification](https://forum.qiime2.org/t/how-to-build-a-tree-with-tips-collapsed-based-on-the-taxonomic-classification/2576)
**Author:** [@bsen2018](https://forum.qiime2.org/u/bsen2018)\ **Replies:** 2\ **Last updated:** [January 18, 2018, 1:31pm UTC](https://forum.qiime2.org/t/how-to-build-a-tree-with-tips-collapsed-based-on-the-taxonomic-classification/2576 "2018-01-18T13:31:44Z")
Hello! I need to generate a phylogenetic tree where the tips are collapsed according to their taxonomic classification with different colours for the taxa. I have already generated the output files from phylogeny (roote… --- ## [Tree visualization](https://forum.qiime2.org/t/tree-visualization/1866)
**Author:** [@Lu\_Yang](https://forum.qiime2.org/u/Lu_Yang)\ **Replies:** 20\ **Last updated:** [December 7, 2017, 7:27pm UTC](https://forum.qiime2.org/t/tree-visualization/1866 "2017-12-07T19:27:40Z")
Hi, I got the rooted.tree from qiime2, but it is a qza file. May I know how to change it into a qzv file, which can be visualized. OR change the qza file into a fasta file, which I can know the reads and draw a tree? Be… --- ## [How do I create a tree from a subset of samples?](https://forum.qiime2.org/t/how-do-i-create-a-tree-from-a-subset-of-samples/1885)
**Author:** [@Lu\_Yang](https://forum.qiime2.org/u/Lu_Yang)\ **Replies:** 7\ **Last updated:** [December 22, 2017, 6:04pm UTC](https://forum.qiime2.org/t/how-do-i-create-a-tree-from-a-subset-of-samples/1885 "2017-12-22T18:04:13Z")
Hi, @thermokarst, Sorry, I have another question about the tree. I use qiime2 and DADA2 demultiplex the 2 batches of samples separately. Then merge the batches rep-seqs.qza, and assign the taxonomy together. But now I… [Next page](https://forum.qiime2.org/tag/tree/131.md?match_all_tags=true&page=1&tags%5B%5D=tree)